Diagnosis of Dysbiosis

Dysbiosis should be suspected if the patient has inflammatory, gastrointestinal, or autoimmune disorders, food intolerance and allergy, colon or breast cancer, unexplained fatigue, neuropsychiatric symptoms, or malnutrition.

The most useful test for diagnosing dysbiosis is a Comprehensive Digestive Stool Analysis (CDSA). CDSA includes the following procedures:


  • Biochemical evaluations of digestion – levels of chymotrypsin, fecal triglycerides, meat and vegetable fibers, fecal pH.
  • Evaluation of intestinal absorption – levels of long and short chain fatty acids, and levels of fecal cholesterol.
  • Metabolic markers of intestinal metabolism – levels of fecal butyrate, levels of beta-glucuronidase, levels of deconjugated bile acids and estrogen within the stool.
  • Evaluation of bacterial microflora, including pathogenic, friendly and imbalanced flora.
  • Detection of abnormal mycology within the large and small intestine.

In order to make CDSA more useful, authors have developed Gut Dysbiosis Score, which we will describe below:

  • 1 point each – excess vegetable fibers, meat, or triglycerides. This can be both the cause and the effect of bacterial overgrowth.
  • 1 point each – excess fatty acids or cholesterol. Indicate malabsorption caused by bacterial overgrowth as it interferes with micelle formation.
  • 2 points each – low concentration of short-chain fatty acids or butyrate. Indicates low anaerobic fermentation of soluble fibers. This is caused either by deficiency of Bifidobacteria or a diet low in soluble fibers.
  • 2 points each – high concentration of short-chain fatty acids or butyrate. Indicates high anaerobic fermentation.
  • 2 pointsalkaline stool pH. Often accompanies low concentration of butyrate. If the butyrate levels are normal, it means that ammonia production is increased, which reflects an excessive activity of urease or a diet high in meat.
  • 3 points eachlack of E. coli or Lactobacillus in stool culture. Direct evidence of dysbiosis.
  • 1 point each – high concentration of atypical Enterobacteriaceae, Klebsiella, Pseudomonas, or Proteus.

Total score of 7 or more strongly indicates clinical dysbiosis; 5-6 – indicates probable dysbiosis; score of 3-4 is borderline.

Additionally, severe cases of dysbiosis may result in abnormal blood tests:


  • Low levels of circulating B12 – caused by malabsorption of this vitamin by the intestine due to damage to its interior lining.
  • Hypoalbuminemia – caused by malabsorption of proteins.
  • Erythrocyte macrocytosis – is caused by the deficiency of B12 and folic acids.